Spectral Modularity Clustering

Implements the network clustering algorithm described in Newman (2006) . The complete iterative algorithm comprises of two steps. In the first step, the network is expressed in terms of its leading eigenvalue and eigenvector and recursively partition into two communities. Partitioning occurs if the maximum positive eigenvalue is greater than the tolerance (10e-5) for the current partition, and if it results in a positive contribution to the Modularity. Given an initial separation using the leading eigen step, 'rSpectral' then continues to maximise for the change in Modularity using a fine-tuning step - or variate thereof. The first stage here is to find the node which, when moved from one community to another, gives the maximum change in Modularity. This node’s community is then fixed and we repeat the process until all nodes have been moved. The whole process is repeated from this new state until the change in the Modularity, between the new and old state, is less than the predefined tolerance. A slight variant of the fine-tuning step, which can improve speed of the calculation, is also provided. Instead of moving each node into each community in turn, we only consider moves of neighbouring nodes, found in different communities, to the community of the current node of interest. The two steps process is repeatedly applied to each new community found, subdivided each community into two new communities, until we are unable to find any division that results in a positive change in Modularity.

Companion Software for the Coursera Statistics with R Specialization

Data and functions to support Bayesian and frequentist inference and decision making for the Coursera Specialization "Statistics with R". See < https://github.com/StatsWithR/statsr> for more information.

This is a Collection of Functions to Analyse Gender Differences

Implementation of functions, which combines binomial calculation and data visualisation, to analyse the differences in publishing authorship by gender described in Day et al. (2020) . It should only be used when self-reported gender is unavailable.

Spatial Analysis and Data Mining for Field Ecologists

Set of tools for reading, writing and transforming spatial and seasonal data, model selection and specific statistical tests for ecologists. It includes functions to interpolate regular positions of points between landmarks, to discretize polylines into regular point positions, link distant observations to points and convert a bounding box in a spatial object. It also provides miscellaneous functions for field ecologists such as spatial statistics and inference on diversity indexes, writing data.frame with Chinese characters.

Fit the Gambin Model to Species Abundance Distributions

Fits unimodal and multimodal gambin distributions to species-abundance distributions from ecological data, as in in Matthews et al. (2014) . 'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are also provided to generate the gambin distribution and for calculating likelihood statistics.

Small Area Estimation using Fay-Herriot Models with Additive Logistic Transformation

Implements Additive Logistic Transformation (alr) for Small Area Estimation under Fay Herriot Model. Small Area Estimation is used to borrow strength from auxiliary variables to improve the effectiveness of a domain sample size. This package uses Empirical Best Linear Unbiased Prediction (EBLUP). The Additive Logistic Transformation (alr) are based on transformation by Aitchison J (1986). The covariance matrix for multivariate application is based on covariance matrix used by Esteban M, Lombardía M, López-Vizcaíno E, Morales D, and Pérez A . The non-sampled models are modified area-level models based on models proposed by Anisa R, Kurnia A, and Indahwati I , with univariate model using model-3, and multivariate model using model-1. The MSE are estimated using Parametric Bootstrap approach. For non-sampled cases, MSE are estimated using modified approach proposed by Haris F and Ubaidillah A .

Hydrologic Model Evaluation and Time-Series Tools

Facilitates the analysis and evaluation of hydrologic model output and time-series data with functions focused on comparison of modeled (simulated) and observed data, period-of-record statistics, and trends.

R Interface to Proximal Interior Point Quadratic Programming Solver

An embedded proximal interior point quadratic programming solver, which can solve dense and sparse quadratic programs, described in Schwan, Jiang, Kuhn, and Jones (2023) . Combining an infeasible interior point method with the proximal method of multipliers, the algorithm can handle ill-conditioned convex quadratic programming problems without the need for linear independence of the constraints. The solver is written in header only 'C++ 14' leveraging the 'Eigen' library for vectorized linear algebra. For small dense problems, vectorized instructions and cache locality can be exploited more efficiently. Allocation free problem updates and re-solves are also provided.

Transparent Assessment Framework for Reproducible Research

Functions to organize data, methods, and results used in scientific analyses. A TAF analysis consists of four scripts (data.R, model.R, output.R, report.R) that are run sequentially. Each script starts by reading files from a previous step and ends with writing out files for the next step. Convenience functions are provided to version control the required data and software, run analyses, clean residues from previous runs, manage files, manipulate tables, and produce figures. With a focus on stability and reproducible analyses, TAF is designed to have no package dependencies. TAF forms a base layer for the 'icesTAF' package and other scientific applications.

Tools to Create, Use, and Convert ecocomDP Data

Work with the Ecological Community Data Design Pattern. 'ecocomDP' is a flexible data model for harmonizing ecological community surveys, in a research question agnostic format, from source data published across repositories, and with methods that keep the derived data up-to-date as the underlying sources change. Described in O'Brien et al. (2021), .